The goal of this proposal is twofold: 1. Identify gene expression changes specific to acute and/or chronic alcohol exposure and subsequent withdrawal in a discovery-based manner that will enhance the understanding of the molecular mechanisms of alcohol-related neuroadaptation. 2. Use DNA microarray technology as a genetic screening tool for Quantitative Trait Loci (QTL) analysis. A QTL is a site on a chromosome which statistically correlates with a trait under study and therefore likely contains a gene or genes which influence that trait. For disorders and complex traits that are inherited in a polygenic or non-Mendalian fashion (influenced by more than one gene or many genes), QTL analysis, recently successfully applied to mice, is currently a common method for mapping mammalian traits. However, once the QM have been mapped, determination of the genes or regulatory elements that underlie these regions of interest remains, for the most part, a formidable task. DNA microarray analysis applied to genetic mapping offers a logical strategy for the detection and validation of important genetic differences that influence a particular trait. The use of congenic strains of mice that have a chromosomal region of interest backcrossed onto a genetic background from a mouse that shows a different phenotype, and vice versa, allows direct comparison at the gene expression level, of that single chromosomal region. The primary objective is to profile genetic differences in brain regiospecific gene expression patterns that exist between C57BL/6J (B6) and DBA/2J (D2) mice (the two strains most commonly used in QTL mapping) as well as B6.D2 and D2.B6 congenic strains. B6 and D2 mouse strains have been extensively utilized in literally tens of thousands of genetic, behavioral, biochemical and pharmacological experiments by the scientific community. Analyzing polymorphisms in brain gene expression between these and several congenic strains will provide information of value to every study that has or will utilize a BXD strategy, including numerous alcohol-related studies. Another aim will be to focus the analysis directly on acute and chronic alcohol withdrawal by using unique selection lines of mice. In this case, microarray analysis will be used to identify genetic as well as alcohol-induced specific differences. Finally, Northerns, RPA, in situ hybridization, and where feasible Western blotting and immuno- histochemistry will be used to verify expression and consequent protein level changes relevant to the QTL mapping and alcohol effect DNA microarray-based analysis. All information on the genetic expression profiling of C57BL/6J and DBA/2J will be freely shared by deposition in the MGI data base (http:/www.informatics.jax.org) as well as the creation of a web site that details both the protocol and results; for an example see: V. Iyer, http://genome-stanford.edu/seruin/).